[gmx-users] gromacs 5.1.2 mdrun can't detect GPU
pall.szilard at gmail.com
Fri Apr 22 21:58:40 CEST 2016
Actually, here's a small program I hacked up that will help diagnose such
issues; you'll find the instructions and explanation of the expected output
in the header of the file:
On Fri, Apr 22, 2016 at 9:32 PM, Szilárd Páll <pall.szilard at gmail.com>
> Don't get me wrong, I don't think anyone was angry at your post - I
> certainly was not. On the contrary, describing this (rather annoying)
> problem and suggesting a solution is of good use for the GROMACS community
> -- and CUDA application user community in general.
> However, it is important to make the correct assessments and draw the
> correct conclusions. Therefore, in order to clarify things, I simply meant
> to point out that the behavior is not a GPU *detection* issue, but a
> software dependency issue. I suggested clarifying this assessment because a
> correct diagnosis will allow the readers of your post (both on this list
> and on your blog) to better understand the problem and seek the appropriate
> solution (to avoid conclusions like GROMACS+CUDA on Ubuntu is problematic
> hence one should use Fedora).
> If you wish to pinpoint the issue at hand, I suggest the following:
> - install an older CUDA version along 7.5, e.g. 6.5
> - grab a simple sample code that uses the CUDA runtime (e.g. from the SDK)
> - compile it with both nvcc's, older and newer,
> - try running both and you'll likely see that the one compiled with the
> newer compiler may fail while the other one will work.
> I hope this helps, let me know if you want to dig further but you get
> On Fri, Apr 22, 2016 at 6:40 PM, Téletchéa Stéphane <
> stephane.teletchea at univ-nantes.fr> wrote:
>> Le 22/04/2016 14:33, Szilárd Páll a écrit :
>>> Additionally, I suggest amending the post to note that the GDK and NVML
>>> that's picked up from it is optional and it is only useful with
>>> Quadro/Tesla cards.
>> Dear Szilárd,
>> I hope I'll find time to produce a proper bug report, but using the
>> Ubuntu binaries
>> with the ubuntu cuda runtime (so exact same version) 352.xx (same for
>> cuda and nvidia driver),
>> gromacs failed to detect the GPU. Up-to-now I have not traced down where
>> the problems lies.
>> This was I think already stated in the previous entry (section at the
>> end: To sum up*
>> avoid ubuntu packages and install upstream drivers and dependencies*.)
>> But since it seems not clear enough I have corrected some typos and added
>> the disclaimer
>> as requested. I hope Gromacs developper do not feel "angry", this was not
>> my goal, I am a long
>> term GNU/Linux contributor and keen to echaustive bug reports. This
>> article was more a short recipe
>> to get it working and not a complaint.
>> I hope the clarifications on the web site are now better, and this it may
>> help others
>> in getting a proprely working installation ...
>> Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein
>> Design In Silico
>> UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322
>> Nantes cedex 03, France
>> Tél : +33 251 125 636 / Fax : +33 251 125 632
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